One explanation for the organism's extreme resistance is the existence of as yet unidentified DNA repair genes in Deinococcus. Another possibility is that Deinococcus uses its redundant, multi-copy genome in ways that other organisms do not. We have published an alternative repair model for D. radiodurans in which the multiple haploid chromosomes are always aligned, thus simplifying the search for repair templates [Minton and Daly, 1995]. The alignment hypothesis is consistent with a small body of circumstantial evidence that includes: i) genetic data showing that D. radiodurans is unable to maintain different DNA markers at the same position on different copies of the main chromosome [Daly and Minton, 1995]. This inability to tolerate heterozygosity applies also to plasmids in D. radiodurans, and strongly supports the existence of a mechanism for continuous genetic 'cross-checking' that is difficult to envision without extensive genomic alignment; and ii) recombination studies also support the aggregation of multi-copy plasmids in Deinococcus [Daly et al., 1994; Daly et al., 1994]. Another hypothesis proposes that the ringlike nucleoids of Deinococcus are key to radiation resistance [Levin-Zaidman et al., 2003]. However, we have shown by transmission electron microscopy that highly compact toroid-shaped nucleoids in D. radiodurans are not necessary for radiation resistance. Alignment of chromosomes could be occurring in the absence of high levels of genomic condensation needed for ringlike nucleoids since alignment of DNA molecules may be a natural consequence of semi-conservative replication in this organism.
Furthermore, it has been shown that chromosomal fragments released by IR-induced DSBs in D. radiodurans appear to be diffusible within condensed nucleoids, where DSB fragments in stationary-phase cells recombined with high efficiency at homologous DSB sites, whether the sites were located adjacently on the same chromosome (Daly and Minton, 1996), separated on different chromosomes (Daly and Minton, 1995) or present on a chromosome and a plasmid (Daly and Minton, 1997). Recent use of electron cryoelectron microscopy of vitreous sections of D. radiodurans supports the conclusion that DNA fragments in D. radiodurans are mobile and that the arrangement of its nucleoids does not play a key role in radioresistance (Eltsov and Dubochet, 2005). Collectively, these broad-based studies have converged on the conclusion that D. radiodurans uses a relatively conventional set of DNA repair and protection functions, but with far greater efficiency than in IR sensitive bacteria.